Fluorine in the structure of Crystal Structure of A Hdac-Like Protein With 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb 2gh6)

The binding sites of Fluorine atom in the structure of Crystal Structure of A Hdac-Like Protein With 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb code 2gh6). This binding sites where shown with 5.0 Angstroms radius around Fluorine atom. The 2gh6 structure was solved by T.K.NIELSEN, C.HILDMANN, D.RIESTER, D.WEGENER, A.SCHWIENHORST, R.FICNER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.8-2.2 Space group P1211 a (A) 68.507 b (A) 94.897 c (A) 123.301 alpha (°) 90.00 beta (°) 104.28 gamma (°) 90.00 Rfactor (%) 15.8 Rfree (%) 21.4 Fluorine Binding Sites: Fluorine binding site 1 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro140, A: Gly141, A: His142, A: His143, A: Gly151, A: Phe152, A: Cys153, A: Asp180, A: Glu309, A: Tyr312, A: Zn9451, A: Cf39452, conact list: Atom Atom Distance (A) F CB A:Pro140 3.92 F CG A:Pro140 3.78 F N A:Gly141 4.95 F NE2 A:His142 3.37 F N A:His142 4.76 F CD2 A:His142 3.25 F CE1 A:His142 4.68 F CG A:His142 4.57 F NE2 A:His143 3.77 F N A:His143 4.69 F CB A:His143 4.60 F ND1 A:His143 4.93 F CD2 A:His143 3.15 F CE1 A:His143 4.79 F CG A:His143 4.04 F O A:Gly151 3.30 F C A:Gly151 4.52 F CB A:Phe152 4.96 F CB A:Cys153 4.84 F SG A:Cys153 3.11 F OD2 A:Asp180 4.75 F OE2 A:Glu309 4.60 F OH A:Tyr312 4.76 F ZN A:Zn9451 4.63 F C9 A:Cf39452 4.29 F C11 A:Cf39452 2.91 F C11 A:Cf39452 3.30 F F2 A:Cf39452 2.16 F O2 A:Cf39452 3.48 F O2 A:Cf39452 2.92 F C13 A:Cf39452 2.42 F C13 A:Cf39452 2.28 F F3 A:Cf39452 0.00 F C15 A:Cf39452 1.33 F F1 A:Cf39452 2.16 interactive model: Fluorine binding site 2 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro140, A: His142, A: His143, A: Gly151, A: Phe152, A: Cys153, A: Asp180, A: Glu309, A: Gly310, A: Tyr312, A: Zn9451, A: Cf39452, A: Hoh9535, conact list: Atom Atom Distance (A) F CB A:Pro140 3.36 F CD A:Pro140 4.27 F CG A:Pro140 2.89 F CA A:Pro140 4.83 F NE2 A:His142 4.85 F CD2 A:His142 4.91 F CD2 A:His143 4.99 F O A:Gly151 4.02 F CB A:Phe152 4.26 F CD1 A:Phe152 3.87 F CE1 A:Phe152 4.80 F CG A:Phe152 4.53 F SG A:Cys153 4.51 F OD2 A:Asp180 4.66 F O A:Glu309 4.78 F C A:Glu309 4.55 F N A:Gly310 4.18 F CA A:Gly310 3.99 F CZ A:Tyr312 4.34 F OH A:Tyr312 3.03 F ZN A:Zn9451 4.53 F C9 A:Cf39452 4.44 F C11 A:Cf39452 3.01 F C11 A:Cf39452 2.97 F F2 A:Cf39452 2.08 F O2 A:Cf39452 2.97 F O2 A:Cf39452 3.60 F C13 A:Cf39452 2.20 F C13 A:Cf39452 2.48 F F3 A:Cf39452 2.16 F C15 A:Cf39452 1.32 F F1 A:Cf39452 0.00 F O A:Hoh9535 3.08 interactive model: Fluorine binding site 3 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro140, A: His142, A: His143, A: Cys153, A: Asp180, A: Asp268, A: Glu309, A: Gly310, A: Tyr312, A: Zn9451, A: Cf39452, A: Hoh9535, conact list: Atom Atom Distance (A) F CB A:Pro140 3.66 F CG A:Pro140 4.01 F NE2 A:His142 3.14 F CD2 A:His142 3.32 F CE1 A:His142 4.35 F CG A:His142 4.59 F NE2 A:His143 4.91 F CD2 A:His143 4.81 F SG A:Cys153 4.83 F CB A:Asp180 4.88 F OD2 A:Asp180 2.90 F OD1 A:Asp180 4.37 F CG A:Asp180 3.85 F OD2 A:Asp268 4.89 F O A:Glu309 4.33 F CB A:Glu309 3.83 F OE2 A:Glu309 3.96 F CD A:Glu309 4.83 F C A:Glu309 3.59 F CG A:Glu309 4.89 F CA A:Glu309 4.05 F N A:Gly310 3.03 F C A:Gly310 4.91 F CA A:Gly310 3.42 F OH A:Tyr312 4.21 F ZN A:Zn9451 3.55 F C9 A:Cf39452 4.96 F C11 A:Cf39452 3.76 F C11 A:Cf39452 3.72 F F2 A:Cf39452 0.00 F O2 A:Cf39452 2.72 F O2 A:Cf39452 2.84 F C13 A:Cf39452 2.39 F C13 A:Cf39452 2.40 F F3 A:Cf39452 2.16 F C15 A:Cf39452 1.31 F F1 A:Cf39452 2.08 F O A:Hoh9535 4.41 interactive model: Fluorine binding site 4 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Pro140, B: Gly141, B: His142, B: His143, B: Gly151, B: Cys153, B: Asp180, B: Glu309, B: Tyr312, B: Zn9551, B: Cf39552, conact list: Atom Atom Distance (A) F CB B:Pro140 3.82 F CG B:Pro140 3.84 F N B:Gly141 4.91 F NE2 B:His142 3.33 F N B:His142 4.80 F CD2 B:His142 3.25 F CE1 B:His142 4.65 F CG B:His142 4.60 F NE2 B:His143 3.60 F N B:His143 4.78 F CB B:His143 4.85 F ND1 B:His143 4.94 F CD2 B:His143 3.15 F CE1 B:His143 4.66 F CG B:His143 4.14 F O B:Gly151 3.27 F C B:Gly151 4.48 F CB B:Cys153 4.93 F SG B:Cys153 3.18 F OD2 B:Asp180 4.78 F OE2 B:Glu309 4.63 F OH B:Tyr312 4.76 F ZN B:Zn9551 4.69 F C9 B:Cf39552 4.34 F C11 B:Cf39552 2.84 F C11 B:Cf39552 3.41 F F2 B:Cf39552 2.16 F O2 B:Cf39552 3.54 F O2 B:Cf39552 2.91 F C13 B:Cf39552 2.45 F C13 B:Cf39552 2.32 F F3 B:Cf39552 0.00 F C15 B:Cf39552 1.35 F F1 B:Cf39552 2.17 interactive model: Fluorine binding site 5 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Pro140, B: His142, B: His143, B: Gly151, B: Phe152, B: Cys153, B: Asp180, B: Glu309, B: Gly310, B: Tyr312, B: Zn9551, B: Cf39552, B: Hoh9570, conact list: Atom Atom Distance (A) F CB B:Pro140 3.43 F CD B:Pro140 4.43 F CG B:Pro140 3.09 F CA B:Pro140 4.92 F NE2 B:His142 4.90 F CD2 B:His143 4.94 F O B:Gly151 3.88 F CB B:Phe152 4.26 F CD1 B:Phe152 3.85 F CE1 B:Phe152 4.79 F CG B:Phe152 4.52 F SG B:Cys153 4.66 F OD2 B:Asp180 4.73 F O B:Glu309 4.95 F C B:Glu309 4.66 F N B:Gly310 4.21 F CA B:Gly310 3.89 F CZ B:Tyr312 4.21 F OH B:Tyr312 2.92 F ZN B:Zn9551 4.54 F C9 B:Cf39552 4.34 F C11 B:Cf39552 3.07 F C11 B:Cf39552 2.91 F F2 B:Cf39552 2.14 F O2 B:Cf39552 2.85 F O2 B:Cf39552 3.60 F C13 B:Cf39552 2.18 F C13 B:Cf39552 2.47 F F3 B:Cf39552 2.17 F C15 B:Cf39552 1.32 F F1 B:Cf39552 0.00 F O B:Hoh9570 3.03 interactive model: Fluorine binding site 6 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Pro140, B: His142, B: His143, B: Cys153, B: Asp180, B: Asp268, B: Glu309, B: Gly310, B: Tyr312, B: Zn9551, B: Cf39552, B: Hoh9570, conact list: Atom Atom Distance (A) F CB B:Pro140 3.72 F CG B:Pro140 4.20 F NE2 B:His142 3.25 F CD2 B:His142 3.53 F CE1 B:His142 4.36 F CG B:His142 4.72 F NE2 B:His143 4.78 F CD2 B:His143 4.86 F SG B:Cys153 4.98 F CB B:Asp180 4.82 F OD2 B:Asp180 2.91 F OD1 B:Asp180 4.18 F CG B:Asp180 3.78 F OD2 B:Asp268 4.86 F O B:Glu309 4.36 F CB B:Glu309 3.80 F OE2 B:Glu309 4.09 F CD B:Glu309 4.90 F C B:Glu309 3.57 F CG B:Glu309 4.85 F CA B:Glu309 4.00 F N B:Gly310 2.94 F C B:Gly310 4.73 F CA B:Gly310 3.28 F OH B:Tyr312 4.22 F ZN B:Zn9551 3.57 F C9 B:Cf39552 4.92 F C11 B:Cf39552 3.68 F C11 B:Cf39552 3.67 F F2 B:Cf39552 0.00 F O2 B:Cf39552 2.73 F O2 B:Cf39552 2.86 F C13 B:Cf39552 2.37 F C13 B:Cf39552 2.39 F F3 B:Cf39552 2.16 F C15 B:Cf39552 1.32 F F1 B:Cf39552 2.14 F O B:Hoh9570 4.36 interactive model: Fluorine binding site 7 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Pro140, C: Gly141, C: His142, C: His143, C: Gly151, C: Phe152, C: Cys153, C: Asp180, C: Glu309, C: Tyr312, C: Zn9651, C: Cf39652, C: Hoh9677, conact list: Atom Atom Distance (A) F CB C:Pro140 3.71 F C C:Pro140 4.98 F CG C:Pro140 3.71 F CA C:Pro140 4.95 F N C:Gly141 4.90 F NE2 C:His142 3.38 F N C:His142 4.77 F CD2 C:His142 3.22 F CE1 C:His142 4.70 F CG C:His142 4.56 F NE2 C:His143 3.72 F N C:His143 4.73 F CB C:His143 4.79 F ND1 C:His143 4.97 F CD2 C:His143 3.18 F CE1 C:His143 4.76 F CG C:His143 4.13 F O C:Gly151 3.42 F C C:Gly151 4.65 F CB C:Phe152 4.98 F CB C:Cys153 4.86 F SG C:Cys153 3.10 F OD2 C:Asp180 4.83 F OE2 C:Glu309 4.40 F OH C:Tyr312 4.84 F ZN C:Zn9651 4.52 F C9 C:Cf39652 4.51 F C11 C:Cf39652 2.99 F C11 C:Cf39652 3.19 F F2 C:Cf39652 2.14 F O2 C:Cf39652 3.56 F O2 C:Cf39652 2.91 F C13 C:Cf39652 2.49 F C13 C:Cf39652 2.24 F F3 C:Cf39652 0.00 F C15 C:Cf39652 1.33 F F1 C:Cf39652 2.16 F O C:Hoh9677 4.99 interactive model: Fluorine binding site 8 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Pro140, C: His142, C: His143, C: Gly151, C: Phe152, C: Cys153, C: Asp180, C: Glu309, C: Gly310, C: Tyr312, C: Zn9651, C: Cf39652, C: Hoh9677, conact list: Atom Atom Distance (A) F CB C:Pro140 3.39 F CD C:Pro140 4.44 F CG C:Pro140 3.05 F CA C:Pro140 4.88 F NE2 C:His142 4.93 F CD2 C:His143 4.93 F O C:Gly151 4.09 F CB C:Phe152 4.26 F CD1 C:Phe152 3.99 F CE1 C:Phe152 4.96 F CG C:Phe152 4.62 F SG C:Cys153 4.59 F OD2 C:Asp180 4.76 F O C:Glu309 4.86 F C C:Glu309 4.57 F N C:Gly310 4.17 F CA C:Gly310 3.89 F CZ C:Tyr312 4.30 F OH C:Tyr312 3.00 F ZN C:Zn9651 4.39 F C9 C:Cf39652 4.39 F C11 C:Cf39652 3.10 F C11 C:Cf39652 2.87 F F2 C:Cf39652 2.08 F O2 C:Cf39652 2.91 F O2 C:Cf39652 3.53 F C13 C:Cf39652 2.20 F C13 C:Cf39652 2.44 F F3 C:Cf39652 2.16 F C15 C:Cf39652 1.31 F F1 C:Cf39652 0.00 F O C:Hoh9677 2.88 interactive model: Fluorine binding site 9 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Pro140, C: His142, C: His143, C: Cys153, C: Asp180, C: Asp268, C: Glu309, C: Gly310, C: Tyr312, C: Zn9651, C: Cf39652, C: Hoh9677, conact list: Atom Atom Distance (A) F CB C:Pro140 3.79 F CG C:Pro140 4.24 F NE2 C:His142 3.29 F CD2 C:His142 3.53 F CE1 C:His142 4.44 F CG C:His142 4.76 F NE2 C:His143 4.80 F CD2 C:His143 4.80 F SG C:Cys153 4.97 F CB C:Asp180 4.91 F OD2 C:Asp180 2.94 F OD1 C:Asp180 4.16 F CG C:Asp180 3.79 F OD2 C:Asp268 4.69 F O C:Glu309 4.35 F CB C:Glu309 3.85 F OE2 C:Glu309 4.06 F CD C:Glu309 4.92 F C C:Glu309 3.56 F CG C:Glu309 4.90 F CA C:Glu309 4.02 F N C:Gly310 2.93 F C C:Gly310 4.71 F CA C:Gly310 3.24 F OH C:Tyr312 4.14 F ZN C:Zn9651 3.33 F C9 C:Cf39652 4.96 F C11 C:Cf39652 3.71 F C11 C:Cf39652 3.69 F F2 C:Cf39652 0.00 F O2 C:Cf39652 2.65 F O2 C:Cf39652 2.75 F C13 C:Cf39652 2.33 F C13 C:Cf39652 2.36 F F3 C:Cf39652 2.14 F C15 C:Cf39652 1.29 F F1 C:Cf39652 2.08 F O C:Hoh9677 4.24 interactive model: Fluorine binding site 10 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Pro140, D: Gly141, D: His142, D: His143, D: Gly151, D: Phe152, D: Cys153, D: Asp180, D: Glu309, D: Tyr312, D: Zn9751, D: Cf39752, conact list: Atom Atom Distance (A) F CB D:Pro140 3.81 F CG D:Pro140 3.68 F N D:Gly141 4.79 F NE2 D:His142 3.44 F N D:His142 4.74 F CD2 D:His142 3.33 F CE1 D:His142 4.75 F CG D:His142 4.67 F NE2 D:His143 3.72 F N D:His143 4.79 F CB D:His143 4.75 F ND1 D:His143 4.98 F CD2 D:His143 3.17 F CE1 D:His143 4.78 F CG D:His143 4.12 F O D:Gly151 3.20 F C D:Gly151 4.44 F CB D:Phe152 4.99 F CD1 D:Phe152 4.96 F CB D:Cys153 4.88 F SG D:Cys153 3.08 F OD2 D:Asp180 4.99 F OE2 D:Glu309 4.57 F OH D:Tyr312 4.74 F ZN D:Zn9751 4.71 F C9 D:Cf39752 4.39 F C11 D:Cf39752 2.86 F C11 D:Cf39752 3.07 F F2 D:Cf39752 2.21 F O2 D:Cf39752 3.54 F O2 D:Cf39752 3.00 F C13 D:Cf39752 2.45 F C13 D:Cf39752 2.23 F F3 D:Cf39752 0.00 F C15 D:Cf39752 1.34 F F1 D:Cf39752 2.19 interactive model: Fluorine binding site 11 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Pro140, D: His142, D: Gly151, D: Phe152, D: Cys153, D: Asp180, D: Glu309, D: Gly310, D: Tyr312, D: Zn9751, D: Cf39752, D: Hoh9785, conact list: Atom Atom Distance (A) F CB D:Pro140 3.43 F CD D:Pro140 4.38 F CG D:Pro140 3.03 F CA D:Pro140 4.93 F NE2 D:His142 4.82 F CD2 D:His142 4.98 F O D:Gly151 4.12 F CB D:Phe152 4.59 F CD1 D:Phe152 3.95 F CE1 D:Phe152 4.74 F CG D:Phe152 4.75 F SG D:Cys153 4.71 F OD2 D:Asp180 4.65 F O D:Glu309 4.64 F C D:Glu309 4.38 F N D:Gly310 3.96 F CA D:Gly310 3.71 F CE2 D:Tyr312 4.97 F CZ D:Tyr312 4.23 F OH D:Tyr312 2.94 F ZN D:Zn9751 4.44 F C9 D:Cf39752 4.41 F C11 D:Cf39752 3.11 F C11 D:Cf39752 2.90 F F2 D:Cf39752 2.15 F O2 D:Cf39752 2.78 F O2 D:Cf39752 3.54 F C13 D:Cf39752 2.16 F C13 D:Cf39752 2.45 F F3 D:Cf39752 2.19 F C15 D:Cf39752 1.33 F F1 D:Cf39752 0.00 F O D:Hoh9785 3.01 interactive model: Fluorine binding site 12 out of 12 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Fluorine in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Pro140, D: His142, D: His143, D: Cys153, D: Asp180, D: Asp268, D: Glu309, D: Gly310, D: Tyr312, D: Zn9751, D: Cf39752, D: Hoh9785, conact list: Atom Atom Distance (A) F CB D:Pro140 3.81 F CG D:Pro140 4.20 F NE2 D:His142 3.01 F ND1 D:His142 4.91 F CD2 D:His142 3.28 F CE1 D:His142 4.17 F CG D:His142 4.50 F NE2 D:His143 4.74 F CD2 D:His143 4.76 F SG D:Cys153 4.88 F CB D:Asp180 4.70 F OD2 D:Asp180 2.96 F OD1 D:Asp180 4.09 F CG D:Asp180 3.69 F OD2 D:Asp268 4.83 F O D:Glu309 4.40 F CB D:Glu309 3.67 F OE2 D:Glu309 3.88 F CD D:Glu309 4.74 F C D:Glu309 3.60 F CG D:Glu309 4.72 F CA D:Glu309 3.94 F N D:Gly310 3.01 F C D:Gly310 4.87 F CA D:Gly310 3.44 F OH D:Tyr312 4.36 F ZN D:Zn9751 3.51 F C11 D:Cf39752 3.73 F C11 D:Cf39752 3.77 F F2 D:Cf39752 0.00 F O2 D:Cf39752 2.73 F O2 D:Cf39752 2.78 F C13 D:Cf39752 2.39 F C13 D:Cf39752 2.41 F F3 D:Cf39752 2.21 F C15 D:Cf39752 1.35 F F1 D:Cf39752 2.15 F O D:Hoh9785 4.58 interactive model: